bioconductor: DESeq2 | Projects | Ecosyste.ms: Papers

10.1186/s12859-020-3506-x

Negative binomial additive model for RNA-Seq data analysis
Cited by: 16
Author(s): Ruwei Xu, Pei Fen Kuan
Software Mentions: 8
Published: over 6 years ago

Genotype-Specific Expression and NLR Repertoire Contribute to Phenotypic Resistance Diversity in Plantago lanceolata
Cited by: 4
Author(s): Pezhman Safdari, Layla Höckerstedt, Mikael Brosché, Jarkko Salojärvi, Anna‐Liisa Laine
Software Mentions: 8
Published: about 5 years ago

10.3389/fgene.2019.01331

Reproducibility of Methods to Detect Differentially Expressed Genes from Single-Cell RNA Sequencing
Cited by: 50
Author(s): Tian Mou, Wenjiang Deng, Fengyun Gu, Yudi Pawitan, Trung Nghia Vu
Software Mentions: 8
Published: over 6 years ago

10.1186/s12864-016-2848-2

ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences
Cited by: 21
Author(s): Wentao Yang, Philip Rosenstiel, Hinrich Schulenburg
Software Mentions: 8
Published: about 10 years ago

10.3389/fpls.2018.00108

Optimization of an RNA-Seq Differential Gene Expression Analysis Depending on Biological Replicate Number and Library Size
Cited by: 61
Author(s): Sophie Lamarre, Pierre Frasse, Mohamed Zouine, Delphine Labourdette, Elise Sainderichin, Guojian Hu, Véronique Le Berre-Anton, Mondher Bouzayen, Élie Maza
Software Mentions: 8
Published: over 8 years ago

10.3389/fgene.2019.00182

Detection of Differentially Expressed Cleavage Site Intervals Within 3′ Untranslated Regions Using CSI-UTR Reveals Regulated Interaction Motifs
Cited by: 9
Author(s): Benjamin J. Harrison, Juw Won Park, Cynthia Gomes, Jeffrey C. Petruska, Matthew R. Sapio, Michael J. Iadarola, Julia H. Chariker, Eric C. Rouchka
Software Mentions: 8
Published: over 7 years ago

10.3389/fnins.2018.00031

Exploring the Complexity of Cortical Development Using Single-Cell Transcriptomics
Cited by: 12
Author(s): Hyobin Jeong, Vijay Tiwari
Software Mentions: 8
Published: over 8 years ago

10.1186/s13059-015-0862-3

Isoform prefiltering improves performance of count-based methods for analysis of differential transcript usage
Cited by: 107
Author(s): Charlotte Soneson, Katarina L. Matthes, Małgorzata Nowicka, Charity W. Law, Mark D. Robinson
Software Mentions: 8
Published: over 10 years ago

10.1186/s12864-018-4649-2

Identification and characterization of functional modules reflecting transcriptome transition during human neuron maturation
Cited by: 15
Author(s): Zhisong He, Qianhui Yu
Software Mentions: 8
Published: over 8 years ago

10.1186/s40168-018-0434-3

Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencing
Cited by: 20
Author(s): Ellen L. Young, Manus Carey, Andrew A. Meharg, Caroline Meharg
Software Mentions: 8
Published: over 8 years ago

10.1038/s41598-018-34019-0

Microbial structure and function in infant and juvenile rhesus macaques are primarily affected by age, not vaccination status
Cited by: 4
Author(s): Yu Hasegawa, Britni Curtis, Vernon Yutuc, Megan Rulien, Kelly Morrisroe, Kristin Watkins, Clayton Ferrier, Chris English, Laura Hewitson, Carolyn M. Slupsky
Software Mentions: 8
Published: almost 8 years ago

10.3390/ijms21010293

Docker4Circ: A Framework for the Reproducible Characterization of circRNAs from RNA-Seq Data
Cited by: 8
Author(s): Giulio Ferrero, Nicola Licheri, Lucia Coscujuela Tarrero, Carlo De Intinis, Valentina Miano, Raffaele Calogero, Francesca Cordero, Michele De Bortoli, Marco Beccuti
Software Mentions: 8
Published: over 6 years ago

10.3389/fgene.2020.573515

SETDB1 Overexpression Sets an Intertumoral Transcriptomic Divergence in Non-small Cell Lung Carcinoma
Cited by: 8
Author(s): Yong‐Kook Kang, Byungkuk Min
Software Mentions: 8
Published: almost 6 years ago

10.1016/j.cell.2019.08.003

Host-Microbe-Drug-Nutrient Screen Identifies Bacterial Effectors of Metformin Therapy
Cited by: 170
Author(s): Rosina Pryor, Povilas Norvaišas, Γεώργιος Μαρίνος, Lena Best, Louise B. Thingholm, Leonor M. Quintaneiro, Wouter De Haes, Daniela Esser, Silvio Waschina, Celia Lujan, Reuben L. Smith, Timothy A. Scott, Daniel Martínez-Martínez, Orla Woodward, Kevin Bryson, Matthias Laudes, Wolfgang Lieb, Riekelt H. Houtkooper, André Franke, Liesbet Temmerman, Ivana Bjedov, Helena M. Cochemé, Christoph Kaleta, Filipe Cabreiro
Software Mentions: 8
Published: about 7 years ago

10.7554/eLife.69937

CLAMP and Zelda function together to promote Drosophila zygotic genome activation
Cited by: 33
Author(s): Jianan Duan, Leila E. Rieder, Megan M Colonnetta, Annie Huang, Mary Mckenney, Scott Watters, Girish Deshpande, William T. Jordan, Nicolas L. Fawzi, Erica Larschan
Software Mentions: 8
Published: about 5 years ago

10.1186/s40168-016-0208-8

Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies
Cited by: 124
Author(s): Jonathan Thorsen, Asker Brejnrod, Martin Steen Mortensen, Morten Arendt Rasmussen, Jakob Stokholm, Waleed Abu Al‐Soud, Søren J. Sørensen, Hans Bisgaard, Johannes Waage
Software Mentions: 8
Published: almost 10 years ago

10.3390/ijms22158285

Maize DNA Methylation in Response to Drought Stress Is Involved in Target Gene Expression and Alternative Splicing
Cited by: 14
Author(s): Qi Wang, Jie Xu, Xuemei Pu, Haozhe Lv, Yanjun Liu, Huihui Ma, Fengkai Wu, Qingjun Wang, Xin Feng, Tianhong Liu, Qinghua Tang, Yanli Lu
Software Mentions: 8
Published: about 5 years ago

10.7554/eLife.51339

Single-cell transcriptome reveals the novel role of T-bet in suppressing the immature NK gene signature
Cited by: 17
Author(s): Chao Yang, Jason R. Siebert, Robert T. Burns, Yongwei Zheng, Ao Mei, Benedetta Bonacci, Demin Wang, Raúl Urrutia, Matthew J. Riese, Sridhar Rao, Karen-Sue Carlson, Monica S. Thakar, Subramaniam Malarkannan
Software Mentions: 7
Published: over 6 years ago

10.7554/eLife.30952

Transcriptomic and proteomic landscape of mitochondrial dysfunction reveals secondary coenzyme Q deficiency in mammals
Cited by: 158
Author(s): Inge Kühl, María Miranda, Ilian Atanassov, Irina Kuznetsova, Yvonne Hinze, Arnaud Mourier, Aleksandra Filipovska, Nils‐Göran Larsson
Software Mentions: 7
Published: almost 9 years ago

10.1371/journal.pcbi.1008329

An extended catalogue of tandem alternative splice sites in human tissue transcriptomes
Cited by: 6
Author(s): Aleksei Mironov, Stepan Denisov, Alexander Greß, Olga V. Kalinina, Dmitri D. Pervouchine
Software Mentions: 7
Published: over 5 years ago

10.7554/eLife.34031

Forniceal deep brain stimulation induces gene expression and splicing changes that promote neurogenesis and plasticity
Cited by: 39
Author(s): Amy E. Pohodich, Hari Krishna Yalamanchili, Ayush T. Raman, Ying-Wooi Wan, Michael C. Gundry, Shuang Hao, Haijing Jin, Jianrong Tang, Zhandong Liu, Huda Y. Zoghbi
Software Mentions: 7
Published: over 8 years ago

10.7554/eLife.51529

Imp/IGF2BP levels modulate individual neural stem cell growth and division through myc mRNA stability
Cited by: 48
Author(s): Tamsin J Samuels, Aino I Järvelin, David Ish‐Horowicz, Ilan Davis
Software Mentions: 7
Published: over 6 years ago

10.1371/journal.pcbi.1008354

Dedicated transcriptomics combined with power analysis lead to functional understanding of genes with weak phenotypic changes in knockout lines
Cited by: 5
Author(s): Chen Xie, Cemalettin Bekpen, Sven Künzel, Maryam Keshavarz, Rebecca Krebs-Wheaton, Neva Škrabar, Kristian K. Ullrich, Wenyu Zhang, Diethard Tautz
Software Mentions: 7
Published: almost 6 years ago

10.1038/s41388-021-01876-5

The FLI portion of EWS/FLI contributes a transcriptional regulatory function that is distinct and separable from its DNA-binding function in Ewing sarcoma
Cited by: 12
Author(s): Megann A. Boone, Cenny Taslim, Julie Crow, Julia Selich‐Anderson, Andrea K. Byrum, Iftekhar A. Showpnil, Benjamin D. Sunkel, Meng Wang, Benjamin Z. Stanton, Emily R. Theisen, Stephen L. Lessnick
Software Mentions: 7
Published: about 5 years ago

10.3389/fgene.2021.664424

Transcriptomes of an Array of Chicken Ovary, Intestinal, and Immune Cells and Tissues
Cited by: 5
Author(s): Eliah Overbey, Theros T Ng, Pietro Catini, Lisa Griggs, Paul A. Stewart, Suzana Tkalčić, R. David Hawkins, Yvonne Drechsler
Software Mentions: 7
Published: about 5 years ago

10.18632/aging.203208

miRNAs generated from Meg3-Mirg locus are downregulated during aging
Cited by: 1
Author(s): Ana-Mihaela Lupan, Evelyn Gabriela Rusu, Mihai Bogdan Preda, Catalina Iolanda Marinescu, Cristina Ivan, Alexandrina Burlacu
Software Mentions: 7
Published: about 5 years ago

10.1371/journal.pbio.3000988

The molecular and metabolic program by which white adipocytes adapt to cool physiologic temperatures
Cited by: 9
Author(s): Hiroyuki Mori, Colleen E. Dugan, Akira Nishii, Ameena Benchamana, Ziru Li, Thomas S. Cadenhead, Arun K. Das, Charles R. Evans, Katherine A. Overmyer, Steven M. Romanelli, Sydney K. Peterson, Devika P. Bagchi, Callie A.S. Corsa, Julie Hardij, Brian S. Learman, Mahmoud El Azzouny, Joshua J. Coon, Ken Inoki, Ormond A. MacDougald
Software Mentions: 7
Published: over 5 years ago

10.1186/s13062-016-0169-7

Sensitivity, specificity, and reproducibility of RNA-Seq differential expression calls
Cited by: 26
Author(s): Paweł P. Łabaj, David P. Kreil
Software Mentions: 7
Published: almost 10 years ago

10.3389/fcell.2021.624053

“All-In-One” Genetic Tool Assessing Endometrial Receptivity for Personalized Screening of Female Sex Steroid Hormones
Cited by: 7
Author(s): Pavel Deryabin, А. П. Домнина, Inga V. Gorelova, M. V. Rulev, М. А. Petrosyan, Nikolay Nikolsky, Aleksandra Borodkina
Software Mentions: 7
Published: over 5 years ago

10.3389/fgene.2018.00250

GUAVA: A Graphical User Interface for the Analysis and Visualization of ATAC-seq Data
Cited by: 15
Author(s): Mayur Divate, Edwin Cheung
Software Mentions: 7
Published: about 8 years ago

10.1186/s12915-021-01062-9

Exposure to ethanol leads to midfacial hypoplasia in a zebrafish model of FASD via indirect interactions with the Shh pathway
Cited by: 12
Author(s): Alfire Sidik, Groves Dixon, Desirè M. Buckley, Hannah G. Kirby, Suwan Sun, Johann K. Eberhart
Software Mentions: 7
Published: about 5 years ago

10.3389/fcell.2021.659294

Ubiquitin Modification Patterns of Clear Cell Renal Cell Carcinoma and the Ubiquitin Score to Aid Immunotherapy and Targeted Therapy
Cited by: 5
Author(s): Peng Zhou, Yuchao Lu, Xiufen Yang, Jin‐Zhou Xu, Chen‐Qian Liu, Qi‐Dong Xia, Junlin Lu, Shaogang Wang, Jia Hu
Software Mentions: 7
Published: over 5 years ago

10.1093/bioinformatics/btu638

HTSeq—a Python framework to work with high-throughput sequencing data
Cited by: 14,991
Author(s): Simon Anders, Paul Theodor Pyl, Wolfgang Huber
Software Mentions: 7
Published: almost 12 years ago

10.15252/embj.2020105565

The RNA polymerase II subunit RPB‐9 recruits the integrator complex to terminate Caenorhabditis elegans piRNA transcription
Cited by: 13
Author(s): Ahmet C. Berkyurek, Giulia Furlan, Lisa Lampersberger, Toni Beltran, Eva-Maria Weick, Emily Nischwitz, Isabela Cunha Navarro, Fabian Braukmann, Alper Akay, Jonathan Price, Falk Butter, Peter Sarkies, Eric A. Miska
Software Mentions: 7
Published: over 5 years ago

10.1186/s13040-017-0150-8

RNA-sequence data normalization through in silico prediction of reference genes: the bacterial response to DNA damage as case study
Cited by: 15
Author(s): Bork A. Berghoff, Torgny Karlsson, Thomas Källman, E. Gerhart H. Wagner, Manfred Grabherr
Software Mentions: 7
Published: about 9 years ago

10.1186/s13040-016-0099-z

SePIA: RNA and small RNA sequence processing, integration, and analysis
Cited by: 22
Author(s): Katherine Icay, Ping Chen, Alejandra Cervera, Ville Rantanen, Rainer Lehtonen, Sampsa Hautaniemi
Software Mentions: 7
Published: over 10 years ago

10.7717/peerj.8103

Acquisition of fungi from the environment modifies ambrosia beetle mycobiome during invasion
Cited by: 33
Author(s): Davide Rassati, Lorenzo Marini, Antonino Malacrinò
Software Mentions: 7
Published: almost 7 years ago

10.1038/s41598-021-94343-w

Gene expression analysis method integration and co-expression module detection applied to rare glucide metabolism disorders using ExpHunterSuite
Cited by: 7
Author(s): Fernando M. Jabato, José Córdoba-Caballero, Elena Rojano, Carlos Romá‐Mateo, Pascual Sanz, Belén Pérez, Diana Gallego, Pedro Seoane, Juan A. G. Ranea, James R. Perkins
Software Mentions: 7
Published: about 5 years ago

10.1093/bioinformatics/btu616

Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking
Cited by: 112
Author(s): Paul J. McMurdie, Susan Holmes
Software Mentions: 7
Published: almost 12 years ago

10.1038/s41598-021-93918-x

Probiotic supplementation reduces inflammatory profiles but does not prevent oral immune perturbations during SIV infection
Cited by: 4
Author(s): Rhianna Jones, Kyle Kroll, Courtney Broedlow, Luca Schifanella, Scott Smith, Brady Hueber, Spandan V. Shah, Daniel R. Ram, Cordelia Manickam, Valerie Varner, Nichole R. Klatt, R. Keith Reeves
Software Mentions: 7
Published: about 5 years ago

10.7717/peerj.11985

Organic farming practices change the soil bacteria community, improving soil quality and maize crop yields
Cited by: 14
Author(s): Ademir Durrer, Thiago Gumière, Maurício Rumenos Guidetti Zagatto, Henrique Petry Feiler, Antônio Marcos Miranda Silva, Rodrigo Henriques Longaresi, Sérgio Kenji Homma, Elke Jurandy Bran Nogueira Cardoso
Software Mentions: 7
Published: almost 5 years ago

10.1038/s41392-021-00703-3

Differential immune responses in pregnant patients recovered from COVID-19
Cited by: 21
Author(s): Ge Chen, Yiming Zhang, Yaoyao Zhang, Jihui Ai, Bin Yang, Mengge Cui, Qiande Liao, Hanxiao Chen, Hualin Bai, Dashing Shang, Jing Chen, Chaoyang Sun, Haiyi Liu, Fengyuan Liu, Biming Mao, Guoqiang Sun, Lu Chen, Jing-wen Lin, Kezhen Li
Software Mentions: 7
Published: about 5 years ago

10.1128/mSystems.00280-19

Extensive Thioautotrophic Gill Endosymbiont Diversity within a Single Ctena orbiculata (Bivalvia: Lucinidae) Population and Implications for Defining Host-Symbiont Specificity and Species Recognition
Cited by: 7
Author(s): Shen Jean Lim, Louie C. Alexander, Annette Summers Engel, Audrey Paterson, Laurie C. Anderson, Barbara J. Campbell
Software Mentions: 7
Published: about 7 years ago

10.1038/s41598-020-77727-2

Gene expression in diapausing rotifer eggs in response to divergent environmental predictability regimes
Cited by: 21
Author(s): Eva Tarazona, José Ignacio Lucas-Lledó, Marı́a José Carmona, Eduardo M. García‐Roger
Software Mentions: 7
Published: almost 6 years ago

10.7717/peerj.9493

Microbial and chemical dynamics of a toxic dinoflagellate bloom
Cited by: 9
Author(s): Nastassia V. Patin, Emily R. Brown, Gabriella Chebli, Claire Garfield, Julia Kubanek, Frank J. Stewart
Software Mentions: 7
Published: about 6 years ago

10.7717/peerj.10836

Fungal and bacterial communities of ‘Pinot noir’ must: effects of vintage, growing region, climate, and basic must chemistry
Cited by: 9
Author(s): Kerri L. Steenwerth, Ian Arthur Morelan, Ruby J. Stahel, Rosa Figueroa‐Balderas, Dario Cantu, Jungmin Lee, Ron C. Runnebaum, Amisha T. Poret-Peterson
Software Mentions: 7
Published: over 5 years ago

10.7717/peerj.8206

consensusDE: an R package for assessing consensus of multiple RNA-seq algorithms with RUV correction
Cited by: 24
Author(s): Ashley J. Waardenberg, Matthew A. Field
Software Mentions: 7
Published: almost 7 years ago

10.1186/s12864-018-5419-x

Dose-dependent impact of oxytetracycline on the veal calf microbiome and resistome
Cited by: 16
Author(s): Bart J. F. Keijser, Valeria Agamennone, Tim J. van den Broek, Martien P. M. Caspers, Adri van de Braak, Richard Bomers, Mieke Havekes, Eric D. Schoen, Martin van Baak, Daniël Mioch, Lonneke Bomers, R.C. Montijn
Software Mentions: 7
Published: over 7 years ago

10.1371/journal.pbio.2004108

Rapid environmental effects on gut nematode susceptibility in rewilded mice
Cited by: 94
Author(s): Jacqueline M. Leung, Sarah A. Budischak, Hao Chung The, Christina Hansen, Rowann Bowcutt, Rebecca Neill, Mitchell Shellman, P’ng Loke, Andrea L. Graham
Software Mentions: 7
Published: over 8 years ago

10.1371/journal.pbio.3000797

An in vitro model of tumor heterogeneity resolves genetic, epigenetic, and stochastic sources of cell state variability
Cited by: 15
Author(s): Corey E. Hayford, Darren R. Tyson, Charles J. Robbins, Peter L. Frick, Vito Quaranta, Leonard A. Harris
Software Mentions: 7
Published: over 5 years ago

10.1038/s41598-020-70173-0

Temperature-dependent life history and transcriptomic responses in heat-tolerant versus heat-sensitive Brachionus rotifers
Cited by: 17
Author(s): Sofia Paraskevopoulou, Alice B. Dennis, Guntram Weithoff, Ralph Tiedemann
Software Mentions: 7
Published: about 6 years ago

10.1038/s41598-020-79296-w

Insights into gene expression changes under conditions that facilitate horizontal gene transfer (mating) of a model archaeon
Cited by: 6
Author(s): Andrea M. Makkay, Artemis S. Louyakis, Nikhil Ram-Mohan, Uri Gophna, J. Peter Gogarten, R. Thane Papke
Software Mentions: 7
Published: over 5 years ago

10.1186/s12920-020-0695-0

Specific chromatin landscapes and transcription factors couple breast cancer subtype with metastatic relapse to lung or brain
Cited by: 20
Author(s): Wesley L. Cai, Celeste B. Greer, Jocelyn F. Chen, Anna Arnal-Estapé, Jian Cao, Qin Yan, Don X. Nguyen
Software Mentions: 7
Published: over 6 years ago

10.1038/s41598-020-70967-2

Transcriptomics uncovers substantial variability associated with alterations in manufacturing processes of macrophage cell therapy products
Cited by: 14
Author(s): Olga L. Gurvich, Katja A. Puttonen, Aubrey Bailey, Anssi Kailaanmäki, Vita Skirdenko, Minna Sivonen, Sanna Pietikäinen, Nigel R. Parker, Seppo Ylä‐Herttuala, Tuija Kekarainen
Software Mentions: 7
Published: about 6 years ago

10.3389/fcell.2021.702046

Transcriptomic Drivers of Differentiation, Maturation, and Polyploidy in Human Extravillous Trophoblast
Cited by: 17
Author(s): Robert Morey, Omar Farah, Sampada Kallol, Daniela F. Requena, Morgan Meads, Matteo Moretto-Zita, Francesca Soncin, Louise C. Laurent, Mana M. Parast
Software Mentions: 7
Published: about 5 years ago

10.1038/s41396-018-0176-z

Long-term in situ permafrost thaw effects on bacterial communities and potential aerobic respiration
Cited by: 64
Author(s): Sylvain Monteux, James T. Weedon, Gesche Blume‐Werry, Konstantin Gavazov, Vincent E. J. Jassey, Margareta Johansson, Frida Keuper, Carolina Olid, Ellen Dorrepaal
Software Mentions: 7
Published: over 8 years ago

10.1242/dev.178590

Maintenance of spatial gene expression by Polycomb-mediated repression after formation of a vertebrate body plan
Cited by: 13
Author(s): Julien Rougeot, Naomi D. Chrispijn, Marco Aben, Dei M. Elurbe, Karolina M. Andralojc, Patrick J. Murphy, Pascal W.T.C. Jansen, Michiel Vermeulen, Bradley R. Cairns, Leonie M. Kamminga
Software Mentions: 7
Published: over 7 years ago

10.3389/fgene.2021.739470

Construction on of a Ferroptosis-Related lncRNA-Based Model to Improve the Prognostic Evaluation of Gastric Cancer Patients Based on Bioinformatics
Cited by: 19
Author(s): Jing Pan, Xinyue Zhang, Xuedong Fang, Zhuoyuan Xin
Software Mentions: 7
Published: about 5 years ago

10.1038/s41598-019-43875-3

Gut microbiome differences between wild and captive black rhinoceros – implications for rhino health
Cited by: 77
Author(s): Keylie M. Gibson, Bryan Nguyen, Laura Neumann, Michele A. Miller, Peter Buss, Savel R. Daniels, Michelle Ahn, Keith A. Crandall, Budhan S. Pukazhenthi
Software Mentions: 7
Published: over 7 years ago

10.1038/s41598-019-44491-x

The LL-100 panel: 100 cell lines for blood cancer studies
Cited by: 67
Author(s): Hilmar Quentmeier, Claudia Pommerenke, Wilhelm G. Dirks, Sonja Eberth, Max Koeppel, Roderick A.F. MacLeod, Stefan Nagel, Klaus G. Steube, Cord C. Uphoff, Hans G. Drexler
Software Mentions: 7
Published: over 7 years ago

10.3389/fgene.2020.00396

Single-Cell Transcriptomic Analysis Reveals Mitochondrial Dynamics in Oocytes of Patients With Polycystic Ovary Syndrome
Cited by: 34
Author(s): Lingbin Qi, Boxuan Liu, Xian Chen, Qiwei Liu, Wanqiong Li, Bo Lv, Xiaoyu Xu, Lu Wang, Qiao Zeng, Jinfeng Xue, Zhigang Xue
Software Mentions: 7
Published: over 6 years ago

10.1038/s41598-019-41940-5

The ciliary Frizzled-like receptor Tmem67 regulates canonical Wnt/β-catenin signalling in the developing cerebellum via Hoxb5
Cited by: 15
Author(s): Zakia Abdelhamed, Dina Abdelmottaleb, Mohammed E. El‐Asrag, Subaashini Natarajan, Gabrielle Wheway, Chris F. Inglehearn, Carmel Toomes, Colin A. Johnson
Software Mentions: 7
Published: over 7 years ago

10.3390/pathogens10010066

Contamination Sources and Transmission Routes for Campylobacter on (Mixed) Broiler Farms in Belgium, and Comparison of the Gut Microbiota of Flocks Colonized and Uncolonized with Campylobacter
Cited by: 8
Author(s): Karolien Hertogs, Annelies Haegeman, Dries Schaumont, Philippe Gelaude, Lieven De Zutter, Jeroen Dewulf, Marc Heyndrickx, Geertrui Rasschaert
Software Mentions: 7
Published: over 5 years ago

10.1038/s41598-019-43274-8

Multiple stressors interact primarily through antagonism to drive changes in the coral microbiome
Cited by: 55
Author(s): Rebecca L. Maher, Mallory M. Rice, Ryan McMinds, Deron E. Burkepile, Rebecca Vega Thurber
Software Mentions: 7
Published: over 7 years ago

10.1186/s12931-020-01392-2

Characterisation of microbiota in saliva, bronchoalveolar lavage fluid, non-malignant, peritumoural and tumour tissue in non-small cell lung cancer patients: a cross-sectional clinical trial
Cited by: 27
Author(s): Rea Bingula, Edith Filaire, Ioana Molnar, Eve Delmas, Jean‐Yves Berthon, Marie‐Paule Vasson, Annick Bernalier-Donadille, Marc Filaire
Software Mentions: 7
Published: about 6 years ago

10.21203/rs.3.rs-438662/v1

Systems biological assessment of human immunity to BNT162b2 mRNA vaccination
Cited by: 2
Author(s): Bali Pulendran, Prabhu S. Arunachalam
Software Mentions: 7
Published: over 5 years ago

10.1038/s41598-018-37746-6

The methylome of the celiac intestinal epithelium harbours genotype-independent alterations in the HLA region
Cited by: 22
Author(s): Nora Fernández-Jiménez, Koldo García-Etxebarria, Leticia Plaza-Izurieta, Irati Romero-Garmendia, Amaia Jauregi-Miguel, María Legarda, Szilvia Ecsedi, Ainara Castellanos–Rubio, Vincent Cahais, Cyrille Cuenin, Davide Degli Esposti, Iñaki Irastorza, Héctor Hernández-Vargas, Zdenko Herceg, José Ramón Bilbao
Software Mentions: 7
Published: over 7 years ago

10.1002/1878-0261.12923

Epigenetic and transcriptional analysis reveals a core transcriptional program conserved in clonal prostate cancer metastases
Cited by: 8
Author(s): Tesa Severson, Yanyun Zhu, Angelo M. De Marzo, Tracy Jones, Jonathan W. Simons, William G. Nelson, Srinivasan Yegnasubramanian, Matthew L. Freedman, Lodewyk F.A. Wessels, Andries M. Bergman, Michael C. Haffner, Wilbert Zwart
Software Mentions: 7
Published: over 5 years ago

10.1016/j.devcel.2017.07.002

The Helicase Aquarius/EMB-4 Is Required to Overcome Intronic Barriers to Allow Nuclear RNAi Pathways to Heritably Silence Transcription
Cited by: 59
Author(s): Alper Akay, Tomás Di Domenico, Kin Man Suen, Amena Nabih, Guillermo E. Parada, Mark Larance, Ragini Medhi, Ahmet C. Berkyurek, Xinlian Zhang, Christopher J. Wedeles, Konrad L. M. Rudolph, Jan Engelhardt, Martin Hemberg, Ping Ma, Angus I. Lamond, Julie M. Claycomb, Eric A. Miska
Software Mentions: 7
Published: about 9 years ago

10.21203/rs.3.rs-131380/v2

Age-dependent pathogenic characteristics of SARS-CoV-2 infection in ferrets
Cited by: 3
Author(s): Young Il Kim, Kwang-Min Yu, June-Young Koh, Eunha Kim, Se‐Mi Kim, Young Ho Kim, Mark Anthony B. Casel, Rare Rollon, Seung-Gyu Jang, Min‐Suk Song, Su‐Jin Park, Hye Won Jeong, Eung‐Gook Kim, Ok-Jun Lee, Younho Choi, Shin-Ae Lee, Su–Hyung Park, Jae U. Jung, Young Ki Choi
Software Mentions: 7
Published: over 5 years ago

10.1186/s12864-021-07593-3

Dense time-course gene expression profiling of the Drosophila melanogaster innate immune response
Cited by: 23
Author(s): Florencia Schlamp, Sofie Y. N. Delbare, Angela M. Early, Martin T. Wells, Sumanta Basu, Andrew G. Clark
Software Mentions: 7
Published: over 5 years ago

10.1186/s12859-018-2370-4

GPrank: an R package for detecting dynamic elements from genome-wide time series
Cited by: 7
Author(s): Hande Topa, Antti Honkela
Software Mentions: 7
Published: almost 8 years ago

10.1186/s12859-020-3433-x

RASflow: an RNA-Seq analysis workflow with Snakemake
Cited by: 30
Author(s): Xiaokang Zhang, Inge Jonassen
Software Mentions: 7
Published: over 6 years ago

10.1186/1471-2105-16-S5-S10

Using epigenomics data to predict gene expression in lung cancer
Cited by: 40
Author(s): Jeffery Li, Travers Ching, Sijia Huang, Lana X. Garmire
Software Mentions: 7
Published: over 11 years ago

10.7554/eLife.59610

Odd-paired is a pioneer-like factor that coordinates with Zelda to control gene expression in embryos
Cited by: 29
Author(s): Theodora Koromila, Fan Gao, Yohei Iwasaki, Peng He, Lior Pachter, J. Peter Gergen, Angelike Stathopoulos
Software Mentions: 7
Published: about 6 years ago

10.1371/journal.pcbi.1006792

IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis
Cited by: 25
Author(s): Brandon Monier, Adam McDermaid, Cankun Wang, Jing Zhao, Allison J. Miller, Anne Fennell, Qin Ma
Software Mentions: 7
Published: over 7 years ago

10.1186/s12864-016-3260-7

DeSigN: connecting gene expression with therapeutics for drug repurposing and development
Cited by: 52
Author(s): Bernard Kok Bang Lee, Kai Hung Tiong, Jit Kang Chang, Chee Sun Liew, Zainal Ariff Abdul Rahman, Aik Choon Tan, Tsung Fei Khang, Sok Ching Cheong
Software Mentions: 7
Published: over 9 years ago

10.1172/jci.insight.139930

Contribution of plasma cells and B cells to hidradenitis suppurativa pathogenesis
Cited by: 88
Author(s): Johann E. Gudjonsson, Lam C. Tsoi, Feiyang Ma, Allison C. Billi, Kelsey R. van Straalen, Allard R. J. V. Vossen, Hessel H. van der Zee, Paul W. Harms, Rachael Wasikowski, Christopher Yee, Syed Monem Rizvi, Xianying Xing, Enze Xing, Olesya Plazyo, Chang Zeng, Matthew Patrick, Margaret M. Lowe, Richard E. Burney, Jeffrey H. Kozlow, Jill R. Cherry-Bukowiec, Yanyun Jiang, Joseph Kirma, Stephan Weidinger, Kelly C. Cushing, Michael D. Rosenblum, Céline C. Berthier, Amanda S. MacLeod, John J. Voorhees, Fei Wen, J. Michelle Kahlenberg, Emanual Maverakis, Robert L. Modlin, Errol P. Prens
Software Mentions: 7
Published: almost 6 years ago

10.1128/AEM.00646-21

Spatial and Temporal Dynamics of Prokaryotic and Viral Community Assemblages in a Lotic System (Manatee Springs, Florida)
Cited by: 8
Author(s): Kema Malki, Natalie A. Sawaya, Michael J. Tisza, Felipe H. Coutinho, Karyna Rosario, Anna J. Székely, Mya Breitbart
Software Mentions: 7
Published: about 5 years ago

10.1186/s12864-018-5390-6

Stability of methods for differential expression analysis of RNA-seq data
Cited by: 14
Author(s): Bingqing Lin, Zhen Pang
Software Mentions: 7
Published: over 7 years ago

10.1016/j.celrep.2019.12.057

Cohesin Disrupts Polycomb-Dependent Chromosome Interactions in Embryonic Stem Cells
Cited by: 118
Author(s): James Rhodes, Angelika Feldmann, Benjamín Hernández-Rodríguez, Noèlia Díaz, Jill M. Brown, Nadezda A. Fursova, Neil P. Blackledge, Praveen Prathapan, Paula Dobrinić, Miles K. Huseyin, Aleksander Szczurek, Kai Kruse, K Nasmyth, Veronica J. Buckle, Juan M. Vaquerizas, Robert J. Klose
Software Mentions: 7
Published: over 6 years ago

10.1186/s42523-021-00117-0

Gut microbiome is affected by gut region but robust to host physiological changes in captive active-season ground squirrels
Cited by: 3
Author(s): Kirsten Grond, Courtney C. Kurtz, Jasmine J. Hatton, Michelle M. Sonsalla, Khrystyne N. Duddleston
Software Mentions: 7
Published: about 5 years ago

10.3390/cells10071576

Transcriptomic Profiling of Femoral Veins in Deep Vein Thrombosis in a Porcine Model
Cited by: 7
Author(s): Leszek Gromadziński, Łukasz Paukszto, Agnieszka Skowrońska, Piotr Holak, Michał Smoliński, Elżbieta Łopieńska–Biernat, Ewa Lepiarczyk, Aleksandra Lipka, J Jastrzebski, Marta Majewska
Software Mentions: 7
Published: about 5 years ago

10.1186/s12859-021-04198-1

Comparative evaluation of full-length isoform quantification from RNA-Seq
Cited by: 12
Author(s): Dimitra Sarantopoulou, Thomas G. Brooks, Soumyashant Nayak, Antonijo Mrčela, Nicholas F. Lahens, Gregory R. Grant
Software Mentions: 7
Published: over 5 years ago

10.1186/s12859-018-2445-2

Empirical assessment of the impact of sample number and read depth on RNA-Seq analysis workflow performance
Cited by: 44
Author(s): Alyssa Baccarella, Claire Williams, Jay Z. Parrish, Charles C. Kim
Software Mentions: 7
Published: almost 8 years ago

10.1016/j.celrep.2020.107930

Pseudo-RNA-Binding Domains Mediate RNA Structure Specificity in Upstream of N-Ras
Cited by: 17
Author(s): Nele Merret Hollmann, Pravin Kumar Ankush Jagtap, Paweł Masiewicz, Tanit Guitart, Bernd Simon, Jan Provazník, Frank Stein, Per Haberkant, Lara Sweetapple, Laura Villacorta, Dylan Mooijman, Vladimı́r Beneš, Mikhail M. Savitski, Fátima Gebauer, Janosch Hennig
Software Mentions: 7
Published: about 6 years ago

10.1186/s12864-021-07489-2

Datura genome reveals duplications of psychoactive alkaloid biosynthetic genes and high mutation rate following tissue culture
Cited by: 5
Author(s): Alex Rajewski, Derreck Carter-House, Jason E. Stajich, Amy Litt
Software Mentions: 7
Published: over 5 years ago

10.1186/s13059-020-02156-3

STARR-seq identifies active, chromatin-masked, and dormant enhancers in pluripotent mouse embryonic stem cells
Cited by: 42
Author(s): Tianran Peng, Yanan Zhai, Yaser Atlasi, Menno ter Huurne, Hendrik Marks, Hendrik G. Stunnenberg, Wout Megchelenbrink
Software Mentions: 7
Published: about 6 years ago

10.1186/s13059-020-02144-7

1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding
Cited by: 32
Author(s): Toby Wilkinson, Daniel Korir, Moses Ogugo, Robert D. Stewart, Mick Watson, Edith Paxton, John P. Goopy, Christelle Robert
Software Mentions: 7
Published: about 6 years ago

10.3389/fmicb.2021.640253

In vitro Fermentation Reveals Changes in Butyrate Production Dependent on Resistant Starch Source and Microbiome Composition
Cited by: 22
Author(s): June Teichmann, Darrell Cockburn
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pgen.1008662

Discovery of novel hepatocyte eQTLs in African Americans
Cited by: 19
Author(s): Yi Zhong, Tanima De, Cristina Alárcon, C. Sehwan Park, Bianca Lec, Minoli Perera
Software Mentions: 7
Published: over 6 years ago

10.1016/j.cell.2016.10.026

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells
Cited by: 527
Author(s): Lu Chen, Bing Ge, Francesco Paolo Casale, Louella Vasquez, Tony Kwan, Diego Garrido-Martín, Stephen Watt, Yan Yan, Kousik Kundu, Simone Ecker, Avik Datta, David Richardson, Frances Burden, Daniel Mead, Alice Mann, José Marı́a Fernández, Sophia Rowlston, Steven P. Wilder, Samantha Farrow, Xiaojian Shao, John Lambourne, Adriana Redensek, Cornelis A. Albers, Vyacheslav Amstislavskiy, Sofie Ashford, Kim Berentsen, Lorenzo Bomba, Guillaume Bourque, David Bujold, Stephan Busche, Maxime Caron, Shu-Huang Chen, Warren A. Cheung, Olivier Delaneau, Emmanouil T. Dermitzakis, Heather Elding, Irina Colgiu, Frederik Otzen Bagger, Paul Flicek, Ehsan Habibi, Valentina Iotchkova, Eva M. Janssen-Megens, Bowon Kim, Hans Lehrach, Ernesto Lowy, Amit Mandoli, Filomena Matarese, Matthew T. Maurano, John A. Morris, Véra Pancaldi, Farzin Pourfarzad, Karola Rehnström, Augusto Rendon, Thomas S. Risch, Nilofar Sharifi, Simon Maguire, Marc Sultan, Alfonso Valencia, Klaudia Walter, Shuang-Yin Wang, Mattia Frontini, Stylianos E. Antonarakis, Laura Clarke, Marie–Laure Yaspo, Stephan Beck, Roderic Guigó, Daniel Rico, Joost H.A. Martens, Willem H. Ouwehand, Taco W. Kuijpers, Dirk S. Paul, Hendrik G. Stunnenberg, Oliver Stegle, Kate Downes, Tomi Pastinen, Nicole Soranzo
Software Mentions: 7
Published: almost 10 years ago

10.1016/j.molcel.2019.01.017

System-wide Profiling of RNA-Binding Proteins Uncovers Key Regulators of Virus Infection
Cited by: 122
Author(s): Manuel García-Moreno, Marko Noerenberg, Shuai Ni, Aino I Järvelin, Esther González-Almela, Caroline E. Lenz, Marcel Bach-Pagés, Victoria Cox, Rosario Avolio, Thomas W. Davis, Svenja Hester, Thibault J.M. Sohier, Bingnan Li, Gregory Heikel, Gracjan Michlewski, Miguel Á. Sanz, Luís Carrasco, Emiliano P. Ricci, Vicent Pelechano, Ilan Davis, Bernd Fischer, Shabaz Mohammed, Alfredo Castelló
Software Mentions: 7
Published: over 7 years ago

10.1016/j.molcel.2021.03.013

Integrated genomic analysis reveals key features of long undecoded transcript isoform-based gene repression
Cited by: 17
Author(s): Amy Tresenrider, Kaitlin Morse, Victoria Jorgensen, Minghao Chia, Hanna Liao, Folkert J. van Werven, Elçin Ünal
Software Mentions: 7
Published: over 5 years ago

10.1186/s12859-019-2599-6

Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data
Cited by: 189
Author(s): Tianyu Wang, Boyang Li, Craig E. Nelson, Sheida Nabavi
Software Mentions: 7
Published: over 7 years ago

10.1098/rsos.160471

Maternal effects and Symbiodinium community composition drive differential patterns in juvenile survival in the coral Acropora tenuis
Cited by: 55
Author(s): Kate M. Quigley, Bette L. Willis, Line K. Bay
Software Mentions: 7
Published: almost 10 years ago

10.1016/j.molcel.2020.01.007

Mammalian RNA Decay Pathways Are Highly Specialized and Widely Linked to Translation
Cited by: 74
Author(s): Alex Tuck, Aneliya Rankova, Alaaddin Bulak Arpat, Luz Angélica Liechti, Daniel Heß, Vytautas Iešmantavičius, Violeta Castelo-Szekely, David Gatfield, Marc Bühler
Software Mentions: 7
Published: over 6 years ago

10.1186/s13059-020-02098-w

Population variation in miRNAs and isomiRs and their impact on human immunity to infection
Cited by: 11
Author(s): Maxime Rotival, Katherine J. Siddle, Martin Silvert, Julien Pothlichet, Hélène Quach, Lluı́s Quintana-Murci
Software Mentions: 7
Published: about 6 years ago

10.1186/s12859-021-04043-5

OmicLoupe: facilitating biological discovery by interactive exploration of multiple omic datasets and statistical comparisons
Cited by: 4
Author(s): Jakob Willforss, Valentina Siino, Fredrik Levander
Software Mentions: 7
Published: over 5 years ago

10.1186/s12859-017-1974-4

CORNAS: coverage-dependent RNA-Seq analysis of gene expression data without biological replicates
Cited by: 14
Author(s): Joel Zi-Bin Low, Tsung Fei Khang, Martti T. Tammi
Software Mentions: 7
Published: almost 9 years ago

Projects: bioconductor: DESeq2

Enhanced Analysis

Science Score: 100/100

Bonuses:

Papers Mentioning DESeq2 9,583